Over the past decades, the amount of DNA sequence information generated and deposited into Genbank has grown exponentially. Many of the next-generation sequencing technologies use a form of sequencing by synthesis (SBS), wherein specially designed nucleotides and DNA polymerases are used to read the sequence of chip-bound, single-stranded DNA templates in a controlled manner. Other next-generation sequencing technologies may use native nucleotides and/or polymerases or labeled oligonucleotides and ligation enzymes to determine nucleic acid sequences. To attain high throughput, many millions of such template spots, each being either single or multiple cloned molecules, are arrayed across a sequencing chip and their sequence is independently read out and recorded.
Sequencing-by-synthesis instruments often use an optical system, such as a microscope, to detect the nucleobase extensions; although non-optical systems are also known. A typical optical instrument uses visible chemical labels to determine the identity of each extended base pair. A typical problem with such systems is that it can be difficult to reliably track the sequencing progress of individual template spots. This is because the template spots are very small, making optical tracking of their positions difficult and sometimes unreliable. A further problem arises when the optical system or sequencing chip are moved during the course of sequencing. In this situation, it is necessary to re-register the chip with the optical system so that the positions of the individual template spots can be re-established after such movement.
The inventors recognized that there is a need for improved fiducial markers, which may be used as a point of reference for ascertaining a measurement of the location of an item, such as a chemical label.